Mex problems on 64bit machine

I have a code which creates a mex file fine on a 32 bit machine but it does not work correctly for a 64 bit machine. The code compiles without errors or warnings however when I run the code I get a segmentation fault.

Does anyone have a suggestion of how to fix this?

Here is the output from the crash.

------------------------------------------------------------------------
       Segmentation violation detected at Wed Aug 10 15:12:08 2011
------------------------------------------------------------------------

Configuration:
  Crash Decoding  : Disabled
  Current Visual  : 0x21 (class 4, depth 24)
  Default Encoding: UTF-8
  GNU C Library   : 2.13 stable
  MATLAB License  : 207107
  MATLAB Root     : /usr/local/MATLAB/R2011a
  MATLAB Version  : 7.12.0.635 (R2011a)
  Operating System: Linux 2.6.38-10-generic #46-Ubuntu SMP Tue Jun 28 15:07:17 UTC 2011 x86_64
  Processor ID    : x86 Family 6 Model 10 Stepping 7, GenuineIntel
  Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode
  Window System   : The X.Org Foundation (11001000), display :0.0

Fault Count: 1

Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 30a3d42800007fd6  RBX = 0000000000000000
  RCX = 00007fd630a456c0  RDX = 0000000000000000
  RSP = 00007fd653276760  RBP = 00007fd653276760
  RSI = 00007fd653276f40  RDI = 00007fd653277004

     R8 = 00007fd62e970440   R9 = 00007fd663749400
    R10 = 00007fd6532765d0  R11 = 00007fd65c61df50
    R12 = 0000000000000002  R13 = 00007fd653277000
    R14 = 00007fd62c0d4b40  R15 = 00007fd653276990

    RIP = 00007fd663795847  EFL = 0000000000010246

     CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):
[  0] 0x00007fd663a48f49 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00474953 fl::sysdep::linux::unwind_stack(void const**, unsigned long, unsigned long, fl::diag::thread_context const&)+000009
[  1] 0x00007fd6639fedc1 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00171457 fl::diag::stacktrace_base::capture(fl::diag::thread_context const&, unsigned long)+000161
[  2] 0x00007fd663a080dd /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00209117
[  3] 0x00007fd663a08364 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwfl.so+00209764 fl::diag::terminate_log(char const*, fl::diag::thread_context const&, bool)+000100
[  4] 0x00007fd662a74be5 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00420837 fl::diag::terminate_log(char const*, ucontext const*, bool)+000085
[  5] 0x00007fd662a71b54 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00408404
[  6] 0x00007fd662a7303d /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00413757
[  7] 0x00007fd662a73197 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00414103
[  8] 0x00007fd662a73b1d /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00416541
[  9] 0x00007fd662a74435 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00418869
[ 10] 0x00007fd6615cac60              /lib/x86_64-linux-gnu/libpthread.so.0+00064608
[ 11] 0x00007fd663795847 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmx.so+00292935 mxgetpr_+000007
[ 12] 0x00007fd625c1f9ea /home/adrianna/Research/mex_lowrank/id_decomp.mexa64+00002538 mexfunction_+000182
[ 13] 0x00007fd65c61dfbc /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmex.so+00049084 mexRunMexFile+000108
[ 14] 0x00007fd65c61af19 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmex.so+00036633
[ 15] 0x00007fd65c61bbbe /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmex.so+00039870
[ 16] 0x00007fd6627e97ef /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_dispatcher.so+00391151 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)+000511
[ 17] 0x00007fd6620f01f0 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01532400
[ 18] 0x00007fd662091975 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01145205
[ 19] 0x00007fd6620ab96e /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01251694
[ 20] 0x00007fd6620b00ec /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01269996
[ 21] 0x00007fd6620adc7a /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01260666
[ 22] 0x00007fd6620ae741 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01263425
[ 23] 0x00007fd6621077d9 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01628121
[ 24] 0x00007fd6627e97ef /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_dispatcher.so+00391151 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)+000511
[ 25] 0x00007fd6620e39b2 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01481138
[ 26] 0x00007fd6620a5e13 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01228307
[ 27] 0x00007fd6620a4eb7 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01224375
[ 28] 0x00007fd6620a5397 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwm_interpreter.so+01225623
[ 29] 0x00007fd662cb38fe /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwbridge.so+00108798
[ 30] 0x00007fd662cb44ae /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwbridge.so+00111790 mnParser+000622
[ 31] 0x00007fd662a5cd39 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00322873 mcrInstance::mnParser_on_interpreter_thread()+000041
[ 32] 0x00007fd662a3fdb2 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00204210
[ 33] 0x00007fd662a3fec0 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00204480
[ 34] 0x00007fd6593e1db6 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmwuix.so+00437686
[ 35] 0x00007fd6593eb13d /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libmwuix.so+00475453
[ 36] 0x00007fd659e370bd /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libuij.so+00217277 sysq::during_F<boost::weak_ptr<sysq::ws_ppeHook>, boost::shared_ptr<sysq::ws_ppeHook> > std::for_each<__gnu_cxx::__normal_iterator<boost::weak_ptr<sysq::ws_ppeHook>*, std::vector<boost::weak_ptr<sysq::ws_ppeHook>, std::allocator<boost::weak_ptr<sysq::ws_ppeHook> > > >, sysq::during_F<boost::weak_ptr<sysq::ws_ppeHook>, boost::shared_ptr<sysq::ws_ppeHook> > >(__gnu_cxx::__normal_iterator<boost::weak_ptr<sysq::ws_ppeHook>*, std::vector<boost::weak_ptr<sysq::ws_ppeHook>, std::allocator<boost::weak_ptr<sysq::ws_ppeHook> > > >, __gnu_cxx::__normal_iterator<boost::weak_ptr<sysq::ws_ppeHook>*, std::vector<boost::weak_ptr<sysq::ws_ppeHook>, std::allocator<boost::weak_ptr<sysq::ws_ppeHook> > > >, sysq::during_F<boost::weak_ptr<sysq::ws_ppeHook>, boost::shared_ptr<sysq::ws_ppeHook> >)+000077
[ 37] 0x00007fd659e38989 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libuij.so+00223625
[ 38] 0x00007fd659e354ae /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/../../bin/glnxa64/libuij.so+00210094 svWS_ProcessPendingEvents(int, int, bool)+000494
[ 39] 0x00007fd662a3e1c7 /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00197063
[ 40] 0x00007fd662a3e60a /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00198154
[ 41] 0x00007fd662a3ed6f /usr/local/MATLAB/R2011a/bin/glnxa64/../../bin/glnxa64/libmwmcr.so+00200047
[ 42] 0x00007fd6615c1d8c              /lib/x86_64-linux-gnu/libpthread.so.0+00028044
[ 43] 0x00007fd66130d04d                    /lib/x86_64-linux-gnu/libc.so.6+00942157 clone+000109

[Adrianna]

Here is the code for the wrapper.

c#include "fintrf.h"
c [T,J,rnorms] = id_decomp(A,INPUT2)
c
c if 0 < INPUT2 < 1
c
c    compute to a given accuracy 
c
c      acc = INPUT2
c
c else
c
c    compute a fixed number of columns
c
c      k   = INPUT2
c
      SUBROUTINE MEXFUNCTION(NLHS, PLHS, NRHS, PRHS)

        IMPLICIT NONE
        INTEGER  PLHS(*), PRHS(*)
        INTEGER  NLHS, NRHS
        INTEGER  mxCreateDoubleMatrix,mxMalloc
        INTEGER  mxGetPr,mxGetM,mxGetN,mxIsComplex
        INTEGER  A_p, INPUT2_p, T_p, rnorms_p, indvec_p, indveci_p
        INTEGER  m, n, k, flag_fixed_k, flag_complex
        REAL*8   INPUT2(1), acc

c     Check that we have two inputs and two or three outputs
      IF (NRHS .NE. 2) THEN
        CALL mexErrMsgTxt('id_decomp requires two input arguments')
      ELSEIF (NLHS .LT. 2) THEN
        CALL mexErrMsgTxt('id_decomp requires 2 or 3 output arguments')
      ELSEIF (NLHS .GT. 3) THEN
        CALL mexErrMsgTxt('id_decomp requires 2 or 3 output arguments')
      ENDIF

c     Extract the problem dimensions from the first input argument.
      m = MXGETM(PRHS(1))
      n = MXGETN(PRHS(1))

c     Assign a pointer to the second input argument.
      INPUT2_p = MXGETPR(PRHS(2))
      CALL mxCopyPtrToReal8(INPUT2_p,INPUT2,1)

c     Check the nature of INPUT2:
c       If INPUT2 <  1, then set acc = INPUT2 and use the "specified accuracy" version of id_idd.
c       If INPUT2 >= 1, then set k   = INPUT2 and use the "specified rank"     version of id_idd.
      IF (INPUT2(1) .LT. 1) THEN
         flag_fixed_k = 0
         k            = min(m,n)
         acc          = INPUT2(1)
      ELSE
         flag_fixed_k = 1
         k            = min(int(INPUT2(1)), min(m,n))
      END IF

c     Check whether the input matrix A is complex.
      flag_complex = mxIsComplex(PRHS(1))
      IF (flag_complex .EQ. 1) THEN
        CALL mexErrMsgTxt('id_decomp cannot yet handle complex input')
      END IF

c     Create the output matrix T and copy A onto T.
      IF (flag_complex .EQ. 0) THEN
        A_p     = mxGetPr(PRHS(1))
        PLHS(1) = mxCreateDoubleMatrix(m,n,0)
        T_p     = mxGetPr(PLHS(1))
        CALL mxCopyPtrToReal8(A_p,%VAL(T_p),m*n)
      END IF

c     Create the vector "rnorms".
c     If there are only 2 output arguments, then it is
c     created simply as a temporary array, otherwise it
c     is created as an output.
      IF (NLHS .EQ. 2) THEN
        rnorms_p = mxMalloc(8*n)
      ELSE
        PLHS(3)  = mxCreateDoubleMatrix(1,n,0)
        rnorms_p = mxGetPr(PLHS(3))
      ENDIF

c     Create an array for the index vector. This is only 
c     a temporary work array since the actual output has
c     to consist of reals to follow matlab standards.
      indveci_p = mxMalloc(4*n)

c     Do the actual computations.
      IF (flag_fixed_k .EQ. 0) THEN
        CALL iddp_id(acc,m,n,%VAL(T_p),k,%VAL(indveci_p),%VAL(rnorms_p))
        CALL mxSetM(PLHS(1),k)
        CALL mxSetN(PLHS(1),n-k)
      ELSE
        CALL iddr_id(m,n,%VAL(T_p),k,%VAL(indveci_p),%VAL(rnorms_p))
        CALL mxSetM(PLHS(1),k)
        CALL mxSetN(PLHS(1),n-k)
      ENDIF

c     Create the REAL VALUED output index vector indvec.
c     Then copy the integer vector indveci to the real valued output indvec.
      PLHS(2)  = mxCreateDoubleMatrix(1,n,0)
      indvec_p = mxGetPr(PLHS(2))
      CALL COPY_IND2REAL(%VAL(indveci_p), %VAL(indvec_p), n)

c     Free the temporary work arrays.
      CALL mxFree(indveci_p)
      IF (NLHS .EQ. 2) THEN
        CALL mxFree(rnorms_p)
      ENDIF

        RETURN
        END

Answer 1

[James Tursa]

You need to strictly follow the API types. You don't get automatic argument type conversion in Fortran like you do in C. Change these lines:

INTEGER PLHS(*), PRHS(*) 
INTEGER NLHS, NRHS 
INTEGER mxCreateDoubleMatrix,mxMalloc 
INTEGER mxGetPr,mxGetM,mxGetN,mxIsComplex 
INTEGER A_p, INPUT2_p, T_p, rnorms_p, indvec_p, indveci_p 
INTEGER m, n, k, flag_fixed_k, flag_complex

To these:

mwPointer PLHS(*), PRHS(*) 
INTEGER*4 NLHS, NRHS 
mwPointer, external :: mxCreateDoubleMatrix,mxMalloc 
mwPointer, external :: mxGetPr
mwSize, external :: mxGetM,mxGetN
INTEGER*4, external :: mxIsComplex 
mwPointer A_p, INPUT2_p, T_p, rnorms_p, indvec_p, indveci_p 
mwSize m, n, k, p
INTEGER*4 flag_fixed_k, flag_complex

And change this line:

k = min(int(INPUT2(1)), min(m,n))

To these:

p = INPUT2(1)
k = min(p, min(m,n))

And change this line:

CALL mxCopyPtrToReal8(INPUT2_p,INPUT2,1)

To these:

p = 1
CALL mxCopyPtrToReal8(INPUT2_p,INPUT2,p)

And change this line:

PLHS(3) = mxCreateDoubleMatrix(1,n,0)

To these:

p = 1
PLHS(3) = mxCreateDoubleMatrix(p,n,0)

And change this line:

PLHS(2) = mxCreateDoubleMatrix(1,n,0)

To these:

p = 1
PLHS(2) = mxCreateDoubleMatrix(p,n,0)

As a side comment, you have some pretty strange code in there for copying mxArray variables and for changing the sizes of pre-existing mxArray variables.

[Adrianna]

Thank you for your quick response.

I have made the suggested changes. However they result in multiple errors when compiling. These errors are in regards to the matlab variable declarations.

For example, in regards to "mwPointer", the error reads "Error: Unclassifiable statement at 1

Am I not linking a necessary file or library?

[Adrianna]

I figured out what was wrong. Thank you again for your help.

[Urankhai]

Hi Adrianna, what was your problem? I have similar one